Get help managing your data

With support from a grant from Force11, the OHSU Library is hosting working sessions to address data management, reproducibility and scientific communication. The sessions are designed to help OHSU students, faculty, and staff understand best practices for managing, publishing, and archiving data.

Session 1: Data Management Open House

OHSU students, faculty, and staff are welcome.

Wednesday, October 9


MRB 310

Happy hour refreshments will be served.

This session will highlight aspects of the data research cycle and introduce challenges and best practices associated with effective data management.

Attendance is not limited but we recommend registering in advance:

Session 2: Hands-on Data Management Consultations

Registration is required* and space is limited. Participants will receive a $50 gift card.

Participants will be asked to bring a yet-to-be published data set and/or publication.  The session will include:

  • A data review to determine which aspects of the data require standardized descriptions for reporting and reproducibility.
  • Analysis of available data repositories and the creation of a deposit plan.
  • Information management strategy, including how to reference key aspects of the data or research context, version control, and linking methods and conclusions to the appropriate data.

*Registration will open after Session 1.

Please contact Jackie Wirz (, 503.494.3443) or Melissa Haendel (, 503.407.5970) for more information.

Your help needed with library journal cancellation decisions

Your help is urgently needed to assist the OHSU Library in deciding which journals OHSU should keep and which ones we should not renew.

Every year the OHSU Library evaluates its journal and database subscriptions to ensure the good stewardship of our budget.  We analyze a variety of data, including publication and citation counts, usage, cost, and community feedback.  The Library adds and cancels journal, database, and book purchases based on this information, with the goal of providing the OHSU community with the resources it needs for research, education, and clinical care.

This year, the Library is also managing chronic increases in journal subscription costs and a smaller budget.  As such, we must ensure that our dollars are being spent on providing the resources most important to the OHSU community.  As part of this process, the following list of journals is being considered for cancellation.  Each title included has demonstrated at least four of the following criteria:

  • Low usage
  • Minimal OHSU publication activity
  • Minimal OHSU citation activity
  • Severe price inflation
  • Not a core journal title.  A core journal title is defined as a title with high OHSU usage and publication activity. A journal is also considered core based on its support of OHSU’s education, research and health care missions.

OHSU community feedback on this list will be used to finalize the Library’s cancellation decisions.  We want to know if there are journals on this list that are important to your work.  Your input is critical, so please review the title list and send your comments to Emily McElroy by September 27, 2013. 

Jackie Wirz, Ph.D., joins Research Roadmap efforts

The OHSU Library is pleased to announce that Jackie Wirz, Ph.D, assistant professor in the OHSU Library, has joined the School of Medicine as a part-time research associate supporting the development of team science, planning and execution of School of Medicine Research Roadmap initiatives, and identification and support of new research endeavors at the school.  The library is excited to extend their partnership with the School of Medicine through Jackie’s appointment.  Chris Shaffer, University Librarian, and Melissa Haendel, Head of the Ontology Development Group, also participate in Research Roadmap taskforces.

In her new role, Jackie will gather, analyze and present data in support of Roadmap projects and assist research leadership in determining and supporting emerging areas of research strength. She’ll also assist faculty leaders in promoting interdisciplinary research.

To date, Dr. Wirz has been involved in the planning and project management of several collaborative research symposia that took place earlier this year. More recently, she’s conducted research and analysis in support of Research Portfolio Workshop activities.

Jackie will continue her work at the OHSU Library as a Bioinformation Specialist, in addition to working on the Research Roapmap. In this way, she can better assist patrons of the OHSU library with her increased understanding of the research efforts at OHSU.

OHSU Library Awarded Funding for Campus and Community Projects

Several OHSU librarians were recently awarded funding from the Pacific Northwest Regional Medical Library for research and projects aimed at understanding and meeting the information needs of our campus and local communities.  The Regional Medical Library (RML) is part of the National Network of Libraries of Medicine program coordinated by the National Library of Medicine.  The program’s mission is to improve the progress of medicine and public health by providing equal access to biomedical information to U.S. health professionals and improving the public’s access to health information.  The OHSU Library has a strong partnership with the RML and we are very proud of the grants described below. 

First Steps in Assessing Oregon Public Health Professional Information Needs This project is designed to evaluate Oregon’s public health professionals’ information needs and better understand the best mechanisms for providing outreach to this community.  For more information contact Laura Zeigen, User Experience Librarian.

Assessing the Health Information Needs of Immigrants and Refugees in Oregon: Potential opportunities for library training

The awardees intend to work with community organizations, including the Immigrant and Refugee Community Organization (IRCO), Sponsors Organized to Assist Refugees (SOAR), and OHSU’s Global Health Center’s Interprofessional Community Health & Education Exchange (iCHEE), to determine if Oregon’s refugee and immigrant populations have health information needs that could be met through library training.  The project will map unmet information needs to potential library education related to health literacy, the National Library of Medicine’s free resources, and other training that may be helpful to members of this population and the people who work with them.  For more information contact Todd Hannon, Reference Librarian.

Investigating the Data and Information Practices of Research Scientists

This project will provide training and resources to research interns on information literacy, and biomedical informatics and tools.  Additionally, instruction will be provided on basic data and information management skills. For more information contact Jackie Wirz, Biomedical Sciences Information Specialist.

Mobile Library Computer Replacement

This OHSU Library will purchase six laptops to provide hands-on training on the use of health information resources around the state of Oregon, replacing the outdated equipment currently used in our mobile computing laboratory.  The awardees will conduct training sessions with OHSU affiliated students & health professionals to evaluate the effectiveness of using the mobile computing laboratory for instruction.  For more information contact Andrew Hamilton, Reference Librarian.


New study shows scientific reproducibility is hampered by lack of specificity of material resources

Written By Nicole Vasilevsky and Melissa Haendel

A key requirement when performing scientific experiments is the accessibility of material resources, including the reagents or model organisms, needed to address a specific hypothesis. The published scientific literature is a source of this valuable information – namely, the name and vendor of an antibody that will pick up a signal on a Western blot, or the description of a mutant zebrafish strain that shows altered development in a specific tissue and time. But frequently the published literature lacks sufficient detail to the extent that researchers are unable to identify material resources used to perform experiments. Biocurators must often chase down authors to identify these resources to support data ingest into public repositories, which is expensive, time consuming, and not sufficiently effective. To highlight to publishers, editors, reviewers, and authors the significance of the problem, we undertook a study to quantify the issue.

Our study, led by Melissa Haendel, Ph.D. and Nicole Vasilevsky, Ph.D. in OHSU Library’s Ontology Development Group, was published on Sept. 5th in the new journal PeerJ. PeerJ is an Open Access publisher with a novel, open approach to peer review and scholarly publishing. Here we demonstrate the magnitude of the problem, which negatively affects the ability of scientists to reproduce and extend published studies. The study shows that a large number of scientific resources are unidentifiable based on the information reported within the journal articles.

Our study examined nearly 240 articles from more than 80 journals spanning five disciplines: neuroscience, immunology, cell biology, developmental biology and general science. The articles were evaluated to determine if the reported material research resources could be uniquely identified based on the information that was provided in each article, its supplemental data, or prior references. Specific criteria were developed to determine if antibodies, cell lines, constructs, model organisms, and knockdown reagents were identifiable. Based on these criteria, our team also developed guidelines for reporting of research resources. These guidelines areavailable online ( and and are being used as a new data standard by authors, reviewers, publishers, and other data contributors to aid reproducibility.

The study showed that just under 50 percent of scientific resources used in previously published articles were unidentifiable, a percentage which varied across resource types and disciplines. While this low value was not unexpected, the actual degree of unidentifiability is still shockingly low. Our study also found no increased level of identification in journals that had more stringent reporting guidelines, suggesting that the reporting guidelines are not strictly adhered to in the evaluation of the research.

The hope is that by quantifying the lack of research reproducibility stemming from inadequate resource identification, that we can highlight to the research and publishing community that there is a significant and pressing need to make material resource information more accessible. The OHSU library is well poised to help researchers with their data management and publishing needs; feel free to contact the library for assistance:

Link to the Published Version of the article (quote this link in your story – the link will ONLY work after the embargo lifts):

PeerJ encourages authors to publish the peer reviews, and author rebuttals, for their article. For the purposes of due diligence by the Press, we can provide these materials as a PDF (and they will be published alongside the final article). Please contact us at to request a copy of the reviews.

Citation to the article:  PeerJ 1:e148 doi: 10.7717/peerj.148

About PeerJ

PeerJ is an Open Access publisher of peer reviewed articles, which offers researchers a lifetime membership, for a single low price, giving them the ability to openly publish all future articles for free. The launch of PeerJ occurred on February 12th, 2013. PeerJ is based in San Francisco, CA and London, UK and can be accessed at

All works published in PeerJ are Open Access and published using a Creative Commons license (CC-BY 3.0). Everything is immediately available—to read, download, redistribute, include in databases and otherwise use—without cost to anyone, anywhere, subject only to the condition that the original authors and source are properly attributed.

For more information, contact:

Nicole Vasilevsky:

Melissa Haendel:

Save Yourself Some Time and Stress! Get to Know a Citation Manager

How many hours of your life have you spent trying to format references at the end of papers or citations within those papers?

If you would like to spend less of your life figuring out if APA style requires a parenthesis here or AMA style requires a comma there, consider taking the time to learn one of the many citation manager tools available.

Citation managers help researchers gather, organize and share references and PDF files found in databases such as PubMed, CINAHL or SCOPUS. You can also use these tools with a word processor to create reference lists and format manuscripts in various styles such as APA, AMA and Vancouver just to name a few.

A selection of these tools can be found at Wikipedia has a comparison of these tools []

Learning any of these tools is useful and will save you time. The OHSU Library has a subscription to a citation manager called RefWorks and can provide in-depth training on this web-based tool, as well as support for others.

Library staff are happy to assist you in determining the best citation manager for your information needs. Please contact your liaison librarian or send a message to for assistance.

New Library Books with OHSU Authors, August 2013

Clinical en face OCT atlas / editors, Bruno Lumbroso…[et al.].

Editor David Huang and contributor Yali Jia affiliated with Oregon Health & Science University.

Medical genetics in pediatric practice / author, American Academy of Pediatrics Committee on Genetics; meditor, Robert A. Saul.

Contributor Robert G. Steiner affiliated with Oregon Health & Science University.

Tarascon adult endocrinology pocketbook / Marc J. Laufgraben and Geetha Gopalakrishnan.

Contributor Kevin C. J. Yuen affiliated with Oregon Health & Science University.

The state of our health 2013 : key health indicators for Oregonians / authors Liana Winett, Claire Gauntner, Thomas Becker, Jenny Mladenovic.

Authors Thomas Becker and Jenny Mladenovic affiliated with Oregon Health & Science University.

Library Closed, Monday, September 2nd, 2013

The OHSU Library will be closed on Monday, September 2, 2013, in observance of Labor Day.

The library will resume regular hours on Tuesday, September 3, 2013.   For additional information on library hours, please see

Nurses Found in the Archives

For years we’ve lamented the fact that there is a relative lack of nursing materials in the OHSU Historical Collections & Archives (HC&A) collections and have sometimes struggled to answer reference questions regarding the school and nurses. To our benefit, Barbara Gaines, R.N., Ed.D., OHSU School of Nursing emerita and author of the history of the school, has seen to it that a steady stream of School of Nursing records and some personal papers have come to us through the years. [i] This summer, Barbara introduced us to Sheila Kodadek, RN, Ph.D, connecting us to another valuable source of nursing history. At the time of her retirement, Sheila was Chair of the Department of Family Nursing and was Associate Dean for Undergraduate Studies. She was also responsible for the development of the BSN program at Western Oregon University.

In my meeting with Sheila, I noticed an invitation to the “Annual OHSU SON Emeritae Luncheon”. Sensing an opportunity, I said in my most inquisitive tone, “Oh, I see that there is a luncheon coming up.”  She asked if I had been invited and when I replied that I had not, she made a call and soon Maija Anderson, (Head of Historical Collections & Archives), and I were on the guest list.

Around 40 emeritae attended the luncheon, including former dean, Carol Lindeman, Ph.D., R.N., F.A.A.N. Interim Dean, Chris Tanner, R.N., Ph.D., F.A.A.N., made announcements and talked about the school’s current state of affairs.  I was invited to make a brief presentation on behalf of HC&A. I talked about the history of the Archives, how they came about, and where we have come since those early days. Following my presentation, each emerita was asked to share something that was meaningful to them during their careers and their comments were recorded. Most poignant were the expressions of dedication and loyalty they felt for each other and for Dean Lindeman. It was obvious that they attributed their successes to each other and to their dean.

I came away even more impressed by nurses than ever before. As the child of a nurse and having had many dealings with nurses over the course of my career as OHSU’s archivist, I have a special place in my heart for these seemingly selfless and devoted women. (I know, I know. There are male nurses too. I have only had the pleasure of working with women.)

As a result of this fortuitous invitation, we have received significant collections from the School of Nursing. In addition to Sheila Kodadek’s papers, we have received donations from Judith Baggs, Ph.D., R.N., F.A.A.N. and Catherine Burns, Ph.D., R.N., C.P.N.P., F.A.A.N. Additional materials from Dean Lindeman are forthcoming. Mary Ann Farnsworth, RN II, also donated her materials. Mary Ann was responsible for the organization and coordination of the OHSU Renal Transplant Body Procurement Program.

We are happy to accept donations from any and all OHSU faculty, staff and students. Our hope is that the word continues to spread that there is a repository where their papers, photos and memorabilia can be donated and where the stories of their lives will not only be preserved, but where researchers will be given access.

Karen Lea Anderson Peterson, MA

Archivist – Assistant Professor

OHSU Historical Collections & Archives

Portland, Oregon

[i] Gaines, Barbara Conway, Oregon Health Sciences University School of Nursing: a history of the school, 1910-1996; Portland, Or.: Oregon Health & Science University School of Nursing, 2002

New Associate University Librarian

Stephanie Kerns, MLS, has joined OHSU as the new Associate University Librarian for Information & Research Services.

Stephanie was most recently the Head of Information and Access Services at Tufts University’s Hirsh Health Science Library. Previously she served as Head of Education and Outreach and Curriculum Librarian at the Galter Health Sciences Library at Northwestern University, where she was also liaison to several programs, including PA, MD, Public Health, Family Medicine, and Prosthetics and Orthotics. She has worked at Georgetown University, University of Southern California, Pepperdine University, and California State University. She received a Masters in Library Science and a Bachelors of Arts in English with a certificate in Women’s Studies, both from Indiana University in Bloomington.

Stephanie is an experienced educator and teacher. She is committed to education in the health sciences, teaching in courses on medical decision making, evidence based medicine, information literacy and problem based learning. She has created faculty development training on topics including copyright, fair use and authors’ rights, EndNote, and using audience response systems effectively.

She has served on curriculum and education committees, and she was a member of the MD Curriculum Renewal Steering Committee at Northwestern University. Stephanie is an active member of the Medical Library Association, currently serving on the MLA Technology Advisory Committee. She regularly publishes and presents on the topic of health sciences education and technology.

Please join the OHSU Library in welcoming Stephanie Kerns to OHSU and Portland.